De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple, Podophyllum hexandrum
© Bhattacharyya et al.; licensee BioMed Central Ltd. 2013
Received: 4 January 2013
Accepted: 19 October 2013
Published: 1 November 2013
The Himalayan or Indian Mayapple (Podophyllum hexandrum Royle) produces podophyllotoxin, which is used in the production of semisynthetic anticancer drugs. High throughput transcriptome sequences or genomic sequence data from the Indian Mayapple are essential for further understanding of the podophyllotoxin biosynthetic pathway.
454 pyrosequencing of a P. hexandrum cell culture normalized cDNA library generated 2,667,207 raw reads and 1,503,232 high quality reads, with an average read length of 138 bp. The denovo assembly was performed by Newbler using default and optimized parameters. The optimized parameter generated 40, 380 assembled sequences, comprising 12,940 contigs and 27,440 singlets which resulted in better assembly as compared to default parameters. BLASTX analysis resulted in the annotation of 40,380 contigs/singlet using a cut-off value of ≤1E-03. High similarity to Medicago truncatula using optimized parameters and to Populus trichocarpa using default parameters was noted. The Kyoto encyclopedia of genes and genomes (KEGG) analysis using KEGG Automatic Annotation Server (KAAS) combined with domain analysis of the assembled transcripts revealed putative members of secondary metabolism pathways that may be involved in podophyllotoxin biosynthesis. A proposed schematic pathway for phenylpropanoids and podophyllotoxin biosynthesis was generated. Expression profiling was carried out based on fragments per kilobase of exon per million fragments (FPKM). 1036 simple sequence repeats were predicted in the P. hexandrum sequences. Sixty-nine transcripts were mapped to 99 mature and precursor microRNAs from the plant microRNA database. Around 961 transcripts containing transcription factor domains were noted. High performance liquid chromatography analysis showed the peak accumulation of podophyllotoxin in 12-day cell suspension cultures. A comparative qRT-PCR analysis of phenylpropanoid pathway genes identified in the present data was performed to analyze their expression patterns in 12-day cell culture, callus and rhizome.
The present data will help the identification of the potential genes and transcription factors involved in podophyllotoxin biosynthesis in P. hexandrum. The assembled transcripts could serve as potential candidates for marker discovery and conservation, which should form the foundations for future endeavors.
Podophyllum hexandrum Royle, commonly referred to as the Himalayan/Indian Mayapple, is an endangered perennial herb belonging to the family Berberidaceae, which is distributed on the lower slopes of the Himalayas in scrub and forest, from Afghanistan to central China. Roots and rhizomes of P. hexandrum contain lignans, such as podophyllotoxin and other related aryltetralin lignans, which are present in Podophyllum spp. but are not restricted to this genus. Extracts of Podophyllum spp. have been used by diverse cultures as antidotes against poisons and as cathartic, purgative, anthelmintic, vesicant and suicidal agents. A crude resin extract of Podophyllum spp., podophyllin, was included in the US Pharmacopoeia in 1820, and this resin has been prescribed to treat venereal warts. Podophyllotoxin has been used as the starting compound for the production of the semi-synthetic drugs etoposide (VP-16-213), teniposide (VM-26) and etopophos, which are used to treat lung and testicular cancers, leukaemia and rheumatoid arthritis. A recent review stated that species containing podophyllotoxin were traditionally used as folk-remedies in China, Japan, India and the United States to treat several illnesses, including gout, tuberculosis, syphilis, warts and various tumors. The Indian species, P. Hexandrum, contains three times more Podophyllotoxin than its American counterpart, P. peltatum, which contains other lignans, such as α- and β-peltatins[7, 8]. However, peltatins do not contribute to the anti-cancer properties of the plant.
To meet the commercial demand, podophyllotoxin has been extracted from the rhizomes of P. hexandrum and P. peltatum collected in the wild. The chemical synthesis of podophyllotoxin is possible, but not economically feasible. Therefore, large quantities of rhizomes have been collected indiscriminately to meet the ever-increasing demands of modern medicine. Severe habitat destruction and over-collection has created acute depletion in the population of this herb. Together with a lack of organized cultivation, this has led to P. hexandrum being classified as a critically endangered species in the Himalayan region[11, 12].
In addition to this genus, other plants, including Linum album, Juniperus chinensis and Callitris drummondii, have been investigated for the in vitro production of podophyllotoxin and its derivatives. However, the production of podophyllotoxin using cell cultures may not be sufficient for biotechnological production systems.
The complete sequences of dirigent protein oxidase (DPO), secoisolariciresinol dehydrogenase (SDG) and cinnamyl alcohol dehydrogenase (CAD) from P. hexandrum have been deposited in the National Centre for Biotechnology Information (NCBI). Lignan biosynthesis involves mechanisms for enantioselective dimerization. DPO affects the selective coupling of the coniferyl alcohol radical to produce (+)-pinoresinol and pinoresinol reductase converts pinoresinol to secoisolariciresinol via lariciresinol. Then, (-)-secoisolariciresinol is converted to (-)-matairesinol by SDG. Matairesinol is a starting point for the biosynthesis of podophyllotoxin. One possible pathway is that matairesinol is converted to yatein and then to podophyllotoxin via deoxypodophyllotoxin. Another direct pathway to podophyllotoxin from matairesinol via thujaplicatin has been proposed. Although the podophyllotoxin biosynthetic pathway is reasonably well characterized and several cDNAs have been reported, the transformation from matairesinol to podophyllotoxin involves hydroxylation, methylations and methylenedioxy bridge formation, and these late steps are yet to be characterized. A recent report revealed two cytochrome P450 enzymes in P. hexandrum and P. peltatum that are capable of converting (-)-matairesinol into (-)-pluviatolide by catalyzing the formation of a methylenedioxy bridge.
De novo transcriptome analysis of next-generation sequencing data is an appropriate technique for identifying unknown genes in non-model organisms. Expressed sequence tag (EST) sequencing, which excludes non-coding and repetitive DNA components, is a cost-effective and frequently used strategy to analyze the transcriptome. Here, we sequenced the transcriptome of P. hexandrum cell culture using the 454 GS-FLX Titanium technology, assembled the raw reads using three assemblers, and chose an assembler with the best performance. Finally, functional annotation, FPKM value, domain analysis, transcription factors (TFs) and simple sequence repeat (SSR) identification, and miRNA targeted transcript identification, were determined. Domains from the identified transcripts that could represent downstream genes encoding enzymes that catalyze the late steps in podophyllotoxin biosynthesis were also identified. The data from this study will form the basis for future studies towards the isolation and characterization of the podophyllotoxin biosynthetic pathway genes from P. Hexandrum.
Results and discussion
454 sequencing of the Mayapple cell culture transcriptome
Overview of sequencing reads and reads after preprocessing
P. hexandrum cell culture sample 454 pyrosequencing
Sequencing reads before preprocessing
Number of HQ reads
Average length of HQ read (bp)
Total length (bp)
Comparison between default and optimized parameters of Newbler
Assembly results of 454 data by using Newbler default and optimized parameters
Newbler (Default parameter)
Newbler (Optimized parameter)
Number of contigs/Singlets
Total bases of contigs/Singlets(bp)
Mean contig/Singlet length
Max Contig/Singlet size
Functional annotation of assembled transcripts and determination of FPKM values
To identify the biological pathways that are active in P. hexandrum cell culture, we mapped the annotated sequences to the reference canonical pathways in KEGG. Among the annotated sequences generated by Newbler using default and optimized parameters, 321 and 1069 unique non-redundant sequences were involved in a particular KEGG pathway of which 32 and 100 unique sequences could be assigned to secondary metabolism respectively (Additional file10 and Additional file11).
Protein domains encoded by the P. hexandrum transcriptome that may represent genes involved in podophyllotoxin biosynthesis
We were interested in probable podophyllotoxin pathway genes that could be identified from the transcriptome, therefore Conserved Domains Database (CDD), Pfam, and Tigr databases were searched for domains encoding CADs, monooxygenases, peroxidases (POD), pinoresinol reductases, DPOs, SDGs, and methyl transferases. Our search identified transcripts coding for domains of CAD, SDG, monooxygenase, POD, methyl transferase, NADB Rossmann superfamily, Flavin utilizing monooxygenases superfamily, Uroporphyrinogen decarboxylase methyltransferase (URO-D CIMS) like superfamily, Isoprene-C2-like reductase (ISOPREN C2) like superfamily, Cytochrome oxidase (CypX) superfamily and Oxidoreductase q1 (Oxidored q1) superfamily (Additional file12 and Additional file13). According to the hypothetical scheme of podophyllotoxin pathway, matairesinol is converted to podophyllotoxin by two consecutive methyl group additions forming a compound like yatein. We were also interested in finding methyl transferases that can transfer two methyl groups to the same substrate at the same time. A Uroporphyrinogen IIIC methyl transferase from P. hexandrum was identified in our previous studies, which is known to function in transferring two methyl groups from S-Adenosyl-L-methionine (SAM) to its substrate[28, 29]. Therefore, in addition to finding SAM dependent methyl transferases, we also identified transcripts encoding URO-D CIMS domains.
Combining KAAS-KEGG pathway analysis with domain searching for phenylpropanoid and probable downstream podophyllotoxin pathway genes
Transcription factors related to secondary metabolism
In silico SSR marker identification
SSRs can be divided into genomic SSRs and EST-SSRs. EST-SSRs are more evolutionary conserved than noncoding sequences and therefore have a relatively high transferability[33, 37]. Next-generation sequencing has identified EST-SSRs in many plant species[38–41]. However, there have been no reports of EST-SSRs in P. hexandrum to date.
SSRs were identified with MISA search tool (http://pgrc.ipk-gatersleben.de/misa/), which is based on the criteria that a dinucleotide or a trinucleotide pattern should appear at least six times, and tetra, penta and hexa nucleotide patterns should appear five times each (Additional file16 for Newbler default, Additional file17 for Newbler optimized). SSR distribution and SSR mining of transcripts identified a total of 1,011 SSRs from 40,380 transcripts, with 94 transcripts containing more than one SSR. The most abundant repeat type was dinucleotides (68.6%) and the dominant tandem repeat motifs were (AT)6 and (AT)7 representing 19.4% and 25.7% respectively.
Transcriptome wide survey of miRNA targets in P. hexandrum cell cultures
MiRNAs are known to regulate many developmental and effector genes at the posttranscriptional level[38, 42]. Using oligonucleotide arrays, miRNAs have been shown to be differentially expressed between tissues and during the maturation of the fruit in the grapevine. Wong et al., predicted three wood related genes, flavonol synthase-like, xyloglucan fucosyltransferase and glucan synthase-like genes to be the targets of miR170, miR172 and miR319, respectively, and suggested that these miRNAs might be directly involved in regulation of the phenylpropanoid pathway and hemicellulose biosynthesis pathway. Downregulation of Flavonol synthase by miR170 would redirect the precursor 4-coumaroyl CoA to lignin biosynthesis.
We identified precursor and mature miRNAs in the P. hexandrum cell culture transcriptome, by searching the contigs and singlet in the public miRNA database (Additional file18 and Additional file19)[41, 45]. Transcripts targeted by miRNAs that are possibly related to phenylpropanoid and podophyllotoxin biosynthesis include cytochrome b6, cytochrome p450 like, cell wall associated hydrolase, cell wall associated protein, laccase, and cytochrome f. Deoxypodophyllotoxin 6-hydroxylase is a cytochrome p450 dependent monooxygenase, that catalyzes the introduction of a hydroxyl group in position 6 of deoxypodophyllotoxin. A cytochrome p450 protein is known to catalyze the biosynthesis of a lignan, (+)- sesamin, by forming two methylenedioxy bridges. Laccases have auxiliary roles in stereoselective coupling to 8-8′ linked lignans.
Comparative qRT-PCR of selected phenylpropanoid pathway genes in cell culture, callus and rhizome and podophyllotoxin accumulation in P. hexandrum cell culture
FPKM values of the transcripts used for qRT-PCR analysis
This report comprises a large, assembled and functionally annotated high throughput genomic resource for P. hexandrum. Our efforts to unravel the probable genes related to the podophyllotoxin biosynthetic pathway using the next-generation whole transcriptome sequencing of P. hexandrum identified almost all the known members of the phenylpropanoid pathway. The annotated transcripts represent a useful resource for subsequent isolation of podophyllotoxin pathway genes in P. hexandrum. In addition to pathway identification, the identification of EST-SSRs as molecular markers will be useful for conservation of P. hexandrum, which is an endangered species.
Sample preparation and 454 pyrosequencing
Calli were induced from mature leaves of P. hexandrum in MS medium supplemented with 2.68 μM Napthyl acetic acid (NAA) and 8.88 μM Benzylaminopurine (BAP). Cell suspension cultures were initiated from freshly subcultured green calli of P. hexandrum in modified liquid MS medium containing 60mM total N content, 1.25 mM potassium dihydrogen phosphate, 6% glucose and 11.41 μM Indole acetic acid (IAA). An inoculum of 5 g cells was used in 50 ml of cell suspension culture medium. Six flasks containing cell suspension cultures were shaken in the dark at 110 rpm for 12 days. The cells were collected by centrifugation at 1000 × g for 5 min, and immediately put in liquid nitrogen and used for RNA isolation. Total RNA was isolated from 12 days old cell suspension cultures using Purelink miRNA isolation kit (Invitrogen, CA, USA). Total RNA was quantified by NanoDrop technology, checked on a 1% denaturing agarose gel and on a bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Removal of rRNA from total RNA was performed using RiboMinus Plant kit for RNA seq (Invitrogen cat. no. A10838-08) using the standard procedure and then concentrated by RiboMinus concentration module (cat no. K155005), according to the manufacturer’s instructions. Library preparation performed using a cDNA Rapid Library Preparation Method Manual-GS FLX Titanium Series, according to the manufacturer’s instructions. For transcriptome sequencing, 1 μg of Ribo-minus total RNA from each sample was used for fragmentation using ZnCl2 solution, followed by ds-cDNA synthesis using a standard cDNA synthesis kit (Roche). This ds-cDNA was then subjected to fragment end-repair followed by adaptor ligation using Rapid Library Prep kit (Roche). emPCR amplification of the cDNA library was performed according to the manufacturer’s instructions (Roche). Clonally amplified cDNA library beads obtained from the emPCR amplification reaction were deposited on a PTP for sequencing using pyrosequencing chemistry. The next-generation sequencing run for whole transcriptome analysis was performed on a Roche 454 GS FLX.
De novo assembly
Raw reads obtained from 454 pyrosequencing were preprocessed by removing low quality reads, and adapter/ primer sequences using PRINSEQ. The high quality reads were uniqed and mapped to non-coding RNA database Rfam (v11.0) using gsMapper. Reads that mapped to ncRNAs sequences were excluded and remaining reads were used for further analysis.The preprocessed reads were then assembled using Newbler with default parameters and optimized parameters. Optimized parameters were set by checking “Use duplicate reads”, “Extend low depth overlaps”, “Reads limited to one contig” and “Single Ace file options”. The sequence data generated in this study have been deposited at NCBI in the Short Read Archive database under the accession (SRX180870 and SRX180386).
Functional annotation, GO mapping, pathway analysis, FPKM value determination and EST-SSR identification
Annotation of the transcripts was carried out using green plants of non-redundant (nr) protein database NCBI using BLASTX. GO mapping was carried out with BLAST 2GO (GO; http://www.geneontology.org). KEGG maps and an enzyme classification number (EC number) were built for pathway analysis. FPKM values for the transcripts were determined using the formula, FPKM = (Number of reads Mapped × 109) / (Length of Transcript × Total Number of Reads). Here number of reads mapped were calculated by mapping reads on assembled transcripts using CLC Genomics Work bench with a mismatch, insertion, deletion cost of 2, 3 and 3 respectively. Potent EST-SSR markers were identified by MISA, a customized Perl script tool freely available for prediction of SSRs.
Protein domains and transcription factor identification in P. hexandrum
Transcripts were searched against a conserved domain database (CDD v3.07) with an E-value cut-off of 0.01 for different domains. For the identification of transcription factor families represented in the P. hexandrum cell culture transcriptome, the transcript contigs were searched against all the transcription factor protein sequences at the plant transcription factor database (http://plntfdb.bio.uni-potsdam.de) using BLASTX with an E-value cutoff 1E-06.
MiRNA target identification in P. hexandrum cell cultures
Conserved miRNAs and their target cDNAs, were found by aligning transcripts against the mature and precursor sequences of known plant miRNAs deposited in miRBase version 19 http://www.mirbase.org/ using CLC Genomic Work bench with a mismatch, insertion, deletion cost of 2, 3 and 3 respectively.
Lignan extraction and high performance liquid chromatography (HPLC) analysis
Lignans were extracted from P. hexandrum cells. In brief, 100 mg of cells were extracted with 2 ml ethanol for 20 min at 60°C in microtubes and sonicated for 15 min. The supernatant was collected after centrifugation and evaporated to dryness under a vacuum. Extracts were dissolved in methanol and used for HPLC analysis. Podophyllotoxin (Sigma-Aldrich, Bangalore, India) was used as a standard. Podophyllotoxin extractions were performed with three biological replicates.
For HPLC, a Waters 2998 photodiode-array detector was set at 290 nm, and separation was carried out using an XTerra RP18, 5 μm, (4.6 × 250 mm i.d.) column. Data analyses were performed with Empower 2 software. Chromatographic conditions were essentially as previously described and standardized in our laboratory.
Quantitative RT-PCR (qRT-PCR)
Total RNA was extracted with a Purelink miRNA isolation kit (Invitrogen) using three biological replicates. RNA (2 μg) was reverse transcribed with oligo(dT) primers using RevertAid H Minus First Strand cDNA Synthesis kit (Fermentas, USA). PCR amplification was performed with Power SYBR Green PCR Master Mix (Applied Biosystems, Japan) on an Applied Biosystems 7500 Real-Time PCR System (Applied Biosystems, USA). Relative expression levels were calculated using the ∆-∆Ct method. All primers for qRT-PCR of selected phenylpropanoid pathway genes have been designed from the sequences obtained from optimized Newbler assembly (Additional file20). Actin primers were designed as reported (Acc. No. FL640971.1), Forward primer: 5′-CTCGGGAGGTGCCACCACC-3′ and Reverse primer 5′-GATGGAAGCTGCTGGGTATTCA-3′.
This work was supported by the CSIR Net Work project (grant No. NWP 0008), project of Council of Scientific and Industrial Research, New Delhi, India. DB, RS acknowledge CSIR and SH to UGC, New Delhi, respectively for their fellowship. The authors acknowledged Director, CSIR-IHBT for providing plant material and Xcelris Labs Ltd, (Ahmedabad, India) for NGS data generation and informatics. We thank Edanz Group Global Ltd. for substantive manuscript copy editing.
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